Fig. 1: Spatial and regulatory genome characteristics of the Kit locus.

a Gene expression in mast cells, melanocytes and mouse embryonic fibroblasts (MEFs) revealed by RNA-seq (n = 3 independent primary cell cultures per group). The height of a column: an expression level in transcripts per million (TPM), the width of a column: an amount of genes with the exact expression level. Genes Pdgfra, Kit, Kdr demonstrate contrasting expression in the chosen cell types. The center mark in the box represents the median, bounded by the 25th and 75th percentiles, and the whiskers are the most extreme data point, which is no more than 1.5 times the interquartile range. Source data are provided as a Source Data file; b Hi-C maps (5 kb resolution) demonstrate that genes Pdgfra, Kit, Kdr are each located in a distinct TAD with minor features being specific to a cell type. Color bars reflect the interaction counts; c Expression and regulatory context of the locus in the cell types. Regions which we refer to as enhancers are highlighted yellow in H3K27ac track; d Research design. Using CRISPR/Cas9 we generated mutant mouse strains with a TAD boundary deletion. The mice were used to obtain primary cell cultures for a further analysis of 3D genome organization and gene expression; e Schematic view of the tissue-specific TAD structures with emphasis on enhancer localisation relative to genes and expression level (silent genes are coloured gray).